3svn: Difference between revisions

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-[[Image:3svn.jpg|left|200px]]
-<!--
+==Crystal structure of mKate S158A mutant at pH 7.5==
-The line below this paragraph, containing "STRUCTURE_3svn", creates the "Structure Box" on the page.
+<StructureSection load='3svn' size='340' side='right'caption='[[3svn]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[3svn]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Synthetic_construct_sequences Synthetic construct sequences]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3SVN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3SVN FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=NRQ:{(4Z)-4-(4-HYDROXYBENZYLIDENE)-2-[3-(METHYLTHIO)PROPANIMIDOYL]-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL}ACETIC+ACID'>NRQ</scene></td></tr>
--->
+<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3svo|3svo]], [[3svr|3svr]], [[3svs|3svs]], [[3svu|3svu]]</div></td></tr>
-{{STRUCTURE_3svn|  PDB=3svn  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3svn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3svn OCA], [https://pdbe.org/3svn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3svn RCSB], [https://www.ebi.ac.uk/pdbsum/3svn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3svn ProSAT]</span></td></tr>
+</table>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Fluorescent proteins that can switch between distinct colors have contributed significantly to modern biomedical imaging technologies and molecular cell biology. Here we report the identification and biochemical analysis of a green-shifted red fluorescent protein variant GmKate, produced by the introduction of two mutations into mKate. Although the mutations decrease the overall brightness of the protein, GmKate is subject to pH-dependent, reversible green-to-red color conversion. At physiological pH, GmKate absorbs blue light (445 nm) and emits green fluorescence (525 nm). At pH above 9.0, GmKate absorbs 598 nm light and emits 646 nm, far-red fluorescence, similar to its sequence homolog mNeptune. Based on optical spectra and crystal structures of GmKate in its green and red states, the reversible color transition is attributed to the different protonation states of the cis-chromophore, an interpretation that was confirmed by quantum chemical calculations. Crystal structures reveal potential hydrogen bond networks around the chromophore that may facilitate the protonation switch, and indicate a molecular basis for the unusual bathochromic shift observed at high pH. This study provides mechanistic insights into the color tuning of mKate variants, which may aid the development of green-to-red color-convertible fluorescent sensors, and suggests GmKate as a prototype of genetically encoded pH sensors for biological studies.
-===Crystal structure of mKate S158A mutant at pH 7.5===
+Molecular Mechanism of a Green-Shifted, pH-Dependent Red Fluorescent Protein mKate Variant.,Wang Q, Byrnes LJ, Shui B, Rohrig UF, Singh A, Chudakov DM, Lukyanov S, Zipfel WR, Kotlikoff MI, Sondermann H PLoS One. 2011;6(8):e23513. Epub 2011 Aug 22. PMID:21887263<ref>PMID:21887263</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-<!--
+</div>
-The line below this paragraph, {{ABSTRACT_PUBMED_21887263}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 3svn" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 21887263 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_21887263}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-[[3svn]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3SVN OCA].
+[[Category: Synthetic construct sequences]]
+[[Category: Byrnes, L]]
-==Reference==
+[[Category: Sondermann, H]]
-<ref group="xtra">PMID:021887263</ref><references group="xtra"/>
+[[Category: Wang, Q]]
-[[Category: Synthetic construct]]
-[[Category: Byrnes, L.]]
-[[Category: Sondermann, H.]]
-[[Category: Wang, Q.]]
 [[Category: Fluorescent protein]]
 [[Category: Fluoresent protein]]
 [[Category: Ph sensor]]